The key here is determining if the .25 ammonia is free ammonia or as I suspect, ammonium. Ammonium is relatively safe. If that’s the case, your other numbers look good. Then, just do water changes (I would do 2/week) and keep Tank clean. It takes time for rot to heal but you should start seeing clear tissue growing which is new tissue. My aquarium water always tests at .25 ammonia. However, I use an extra test kit, Seachem Free & Total which indicates 0 of free ammonia. I also use an ammonia alert on my tanks by Seachem. It lasts about a year and quickly alerts you if any free ammonia in the water. My is always in the safe zone although my API test kit indicates .25ppm ammonia. You may want to invest in these 2 items. Relatively inexpensive and worth the money. As essjay was attempting to explain above, a PH of 8 still keeps the ammonia level at more ammonium than ammonia. However, he indicated this was free ammonia and it is not. Due to the fact that your tank has been cycling, your PH may be a little higher than normal. Continue to test and hopefully you will see the PH drop a little. This You Tube video may help explain better. Good luck!